Horizontal gene transfer in ferns
Ferns have adapted the ability to thrive in the shade of the forest floor. Recently, this adaptation has been linked to horizontal gene transfer of a nuclear gene. Plants use photoreceptor systems to carry out their biological processes. The most common receptors use either UV-blue or red/far-red light, but the neochrome is a chimeric receptor. This means that is a fusion of both photoreceptors and is able to process both types of light. The neochrome is an example of convergent evolution, arising in both algae and ferns independently 1. The neochrome is very rare in plants and is most likely the reason why ferns are able to survive in the low-light of the forest floor1,2. Ferns and lycophytes are unique land plants that exist with both diploid sporophyte and haploid gametophyte at the same time. All other land plants alternate between the two phases in their sexual life cycle. Furthermore ferns gametophytes grow in direct contact with the environment 2. Experimental Design Li et al data mined previously identified sequences (and some new). They searched for neochrome orthologs across many different species. The list below highlights their searches: * 433 Transcriptome sequences from the One Thousand Plants Project ** Brown, red, and green algae ** Bryophytes (Hornwort) ** Lycophytes ** Ferns ** Seed plants ** They sequenced the transcriptome of Pteridium aquilinum *** A type of fern * Used 40 whole or draft genomes of plants and algae Evidence of Horizontal Gene Transfer The algal neochrome had previously only been identified in one species of green algae, Mougeotia scalaris 1,2. This study also identified neochrome in the ''Zygnemataceae ''clade. Li et al were surprised to find the neochrome gene in Hornwort (pictured left). The divergence of the bryophytes, hornwort, liverwort, and mosses, is still debated. Since this was a surprising find the authors isolated the genes from the 5 hornwort genomes using PCR and cloning. To further verify this result and rule out contamination they perfomred "genome-walking" in one species and found a hornwort gene downstream. There are three possible explanations from neochrome in land plants (only found in ferns and hornworts): # Ancient origin at branch point of hornworts and tracheophytes (ferns), followed by loss of gene by lycophytes and seed plants # Independent origins, i.e. convergent evolution # One or more horizontal gene transfers (HGT) Using sequence alignments of phototropin (UV-blue) and phytochrome (red/far-red) photoreceptor systems along with the fern and hornwort neochromes they generated a phylogeny tree. The nested relationship suggests HGT and Bayesian estimates supported HGT over the the other possibilities. To help support the HGT hypothesis they used information from fossils and a statistical model to estimate the point of divergence of hornworts and ferns neochrome genes. Previous publications have found the hornworts and ferns diverged at least 400 million years ago. Li et al found that the neochrome genes diverged about 179 million years ago. Furthermore the single hornwort photoropin gene has no introns. This suggests that gene fuison occured between the phytochrome an photoropin in hornworts via a retrotransposon. The phototropin genes in ferns do contain introns. This again supports the HGT model. It also appears that there are multiple HGT in ferns themselves. The branches on the tree for fern neochrome do not follow the divergence of fern species. After checking their model for bias Li et al proposed three explanations: # Reoccurring HGT events # an elevated gene turnover rate # combination of the two Conclusions The HGT in ferns is interesting because it has allowed them to survive and flourish on the bottom of the forest floor. This transfer also suggests convergent evolution of the neochrome in the marine and terrestrial species. It was a good topic for this article because in the end it appears to be numerous HGTs of the neochrome between different fern species. The sexual cycle of the fern allows for HGT readily. References 1 Suetsugu, N. et al. 2005. PNAS. 102:3705-9 PMID:16174755 2 Li et al. 2014. PNAS. 111:6672-7 PMID:24733898